Linkage disequilibrium in the human genome

David E. Reich (), Michele Cargill, Stacey Bolk, James Ireland, Pardis C. Sabeti, Daniel J. Richter, Thomas Lavery, Rose Kouyoumjian, Shelli F. Farhadian, Ryk Ward and Eric S. Lander
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David E. Reich: Whitehead Institute / MIT Center for Genome Research
Michele Cargill: Whitehead Institute / MIT Center for Genome Research
Stacey Bolk: Whitehead Institute / MIT Center for Genome Research
James Ireland: Whitehead Institute / MIT Center for Genome Research
Pardis C. Sabeti: Institute of Biological Anthropology, University of Oxford
Daniel J. Richter: Whitehead Institute / MIT Center for Genome Research
Thomas Lavery: Whitehead Institute / MIT Center for Genome Research
Rose Kouyoumjian: Whitehead Institute / MIT Center for Genome Research
Shelli F. Farhadian: Whitehead Institute / MIT Center for Genome Research
Ryk Ward: Institute of Biological Anthropology, University of Oxford
Eric S. Lander: Whitehead Institute / MIT Center for Genome Research

Nature, 2001, vol. 411, issue 6834, 199-204

Abstract: Abstract With the availability of a dense genome-wide map of single nucleotide polymorphisms (SNPs)1, a central issue in human genetics is whether it is now possible to use linkage disequilibrium (LD) to map genes that cause disease. LD refers to correlations among neighbouring alleles, reflecting ‘haplotypes’ descended from single, ancestral chromosomes. The size of LD blocks has been the subject of considerable debate. Computer simulations2 and empirical data3 have suggested that LD extends only a few kilobases (kb) around common SNPs, whereas other data have suggested that it can extend much further, in some cases greater than 100 kb4,5,6. It has been difficult to obtain a systematic picture of LD because past studies have been based on only a few (1–3) loci and different populations. Here, we report a large-scale experiment using a uniform protocol to examine 19 randomly selected genomic regions. LD in a United States population of north-European descent typically extends 60 kb from common alleles, implying that LD mapping is likely to be practical in this population. By contrast, LD in a Nigerian population extends markedly less far. The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked demographic event about 27,000–53,000 years ago.

Date: 2001
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DOI: 10.1038/35075590

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